Reference: Fukuzawa, Oki, Hosaka, Sugasawa, and Kikuchi, Org.

Since its introduction in 1988, the Simplified Molecular Input Line Entry System (SMILES) has become one of the most widely-used molecular encoding systems in cheminformatics. But all technologies, no matter how widely-used, can be improved, and SMILES is no exception. This article, the first in a series, discusses a particularly thorny problem in the SMILES language.

Of all the components that make up today’s cheminformatics systems, the 2D structure editor may be the most widely-used. A 2D structure editor is often a chemist’s first and most enduring exposure to cheminformatics, and can be encountered as early as Junior High or High School. Over time, a good 2D structure editor becomes every bit as important to a chemist as a text editor is to a writer or software developer.

Previously, I described an unsuccessful first attempt to compile the popular cheminformatics C/C++ library Open Babel to pure Java bytecode using NestedVM. This article follows that topic one step further, and shows how to obtain a runnable Java classfile. Although major functionality is missing, the principle of compiling arbitrary C/C++ code to both Java source code and Java bytecode is illustrated.

My kind of tutorial: pick something unexpected but useful, start from the beginning, be specific, and show lots of pictures.

Rubidium is a Ruby cheminformatics scripting environment. Previously, a problem was reported with the RubyForge gem repository that prevented the simple installation of the Rubidium gem. After filing a bug report, the problem was resolved. The problem, which led to a 404 being issued when trying to install the gem from the remote RubyGems repository, was a variant of a known RubyForge issue.

From the early days, Java has been described by Sun as the “write once, run anywhere” language and platform. And for the most part, Sun has made good on this promise. It’s taken some time, but today’s Java Virtual Machines (JVMs) enable developers to feel very confident of their code executing as designed (and unmodified) on any computer system. It’s easy to forget, but that’s a Big Deal.

Wouldn’t it be great to be able to compile code written in languages like FORTRAN, C, and C++ to Java bytecode? NestedVM - almost magically - can do just that. This article documents a failed first attempt to compile the popular cheminformatics toolkit Open Babel, which is written in C and C++, to pure Java bytecode with NestedVM.

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